* The court-martial trial of three SEALs accused of committing war crimes began with a flurry of motions Monday morning inside the courtroom of Naval Base San Diego.

* Special Warfare Operator 1st Class Daniel V. Dambrosio Jr. and two Special Operator Chief Petty Officers — Xavier Silva and David N. Swarts — stand accused of abusing unknown male prisoners at Village Stability Platform Kalach in the Chora District of Afghanistan’s Uruzgan Province on May 31, 2012.

* A trial for their commander, Navy Lt. Jason L. Webb, waits in the wings.

The Navy’s top attorney might have scuttled a war crimes case against three SEALs by unlawfully meddling behind the scenes to bring charges against them.

After a flurry of Monday motions in the courtroom of Navy Cmdr. Arthur Gaston, the military judge ruled that Vice Adm. James Crawford III — the Navy’s judge advocate general — appears to have exerted unlawful command influence in a case first brought to light by a 2015 story in The New York Times.

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The burden now shifts to military prosecutors to prove that Crawford, Naval Special Warfare Command’s Rear Adm. Timothy Szymanski and other senior leaders did not create the appearance of behind-the-scenes maneuvers.

In the case at hand, Special Warfare Operator 1st Class Daniel V. Dambrosio Jr. and two Special Operator Chief Petty Officers — Xavier Silva and David N. Swarts — are accused of abusing male prisoners at Village Stability Platform Kalach in the Chora District of Afghanistan’s Uruzgan Province on May 31, 2012.

A June trial for their commander, Navy Lt. Jason L. Webb, waits in the wings but could be scuttled by the judge’s ruling, too.

It’s now the third time Crawford has been accused of unlawfully plotting with military leaders to convict SEALs.

A ruling is expected in the coming days from the U.S. Court of Appeals for the Armed Forces in Washington, D.C., into Crawford’s alleged involvement in the rape case of Senior Chief Special Warfare Operator Keith Barry, who was court-martialed and convicted in San Diego in 2015.

A special judge hearing evidence in Barry’s appeal already ruled that Crawford and others unlawfully tampered in the matter but left the final adjudication to the higher court.

Crawford also was accused by defense attorneys of unlawfully inserting himself into a probe involving the May 6, 2016, pool drowning of Seaman James Derek Lovelace during initial SEAL training. He has long insisted he was innocent in those cases and declined comment on Monday.

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“The prosecution has opposed the defense motion to dismiss based on unlawful command influence in US v. Dambrosio, Silva and Swartz, and the judge’s ruling on the matter is forthcoming,” Navy spokeswoman Patricia Babb said by email. “It would be inappropriate to discuss this case further, as it is Navy policy to not comment on ongoing or pending litigation.”

Military prosecutors suspect that the three SEALs and several village militiamen began committing war crimes hours after a bomb detonated at an Afghan Local Police checkpoint.

Called “ALP,” they were part of an ad hoc mix of armed militiamen that fall under the control of Kabul’s Interior Ministry but often are trained and led by SEALs or Army Green Berets.

Angered by the death of one of their militiamen in the blast, the Afghan police unit detained a group of Afghan men and marched them to the American compound near Kalach, kicking them and beating them with rifle butts and car antennas, according to witness statements compiled in a Navy Criminal Investigative Service report.

Relying on the recollections of four American soldiers, two Navy support personnel and a local Afghan police officer who allegedly witnessed and reported parts of the incident, prosecutors believe that Dambrosio, Silva and Swarts joined in with the militiamen and, by the end of the night, one Afghan prisoner died.

An Army witness later claimed that a senior Afghan police officer told him that the prisoners, including the dead detainee, were innocent.

The NCIS probe determined that Dambrosio, of Naval Special Warfare Group Training Detachment, assaulted one unknown man by grabbing his throat and striking his chest with a rock. He also pulled out his service pistol, placed it near a bound prisoner’s head and fired it in order to terrify him, military investigators say.

A member of Special Reconnaissance Team 2, Silva allegedly dragged an unidentified detainee by the neck, struck his chest with a rock, kicked him and at one point placed his body weight on his body to crush him.

Likewise accused of firing his pistol near a prisoner’s head, SEAL Team 5’s Swarts also allegedly struck a man with a rock. He’s also been charged with conspiring with his commander, SEAL Team 10’s Lt. Jason L. Webb, to lie to military leaders about what really happened that night.

Prosecutors allege that Swarts and Webb discussed filing a fake statement with their superiors and mulled submitting alternative versions of what really happened, omitting key details in their official report.

Because he was the senior SEAL during the incident, Webb’s charges are the most serious.

Along with the conspiracy count, he’s accused of willfully failing to supervise the interactions between his sailors and the Afghan militiamen when they interrogated the prisoners. Instead, Webb retreated to his office for “the duration of the interactions to avoid supervising the situation and the U.S. personnel,” according to his charge sheet.

Instead of sending a report warning his chain of command about the alleged war crimes, he sent a bogus message indicating only that an Afghan militiaman died in an explosion and that the village police officers’ “swift actions, decision making, and communication skills reflect that they are well prepared to handle situations of this magnitude,” court filings state.

He also allegedly urged an Army staff sergeant to never talk about how the SEALs abused the prisoners, part of an effort to impede a criminal probe, federal agents believe.

Not that it initially mattered because neither Webb nor his men ended up at a court-martial in 2012, after allegations of the war crimes surfaced.

Their commander, Capt. Robert E. Smith, gave them non-judicial punishment. Called a “Captain’s Mast” in the Navy, it’s a far less severe form of justice and its proceedings play out in private, far from public courtrooms and a paper trail citizens can follow.

Smith later said that he believed some of the statements against the SEALs were shaky and senior staff advisers had urged him to forgo what’s called “Article 32” proceedings, which are similar to a grand jury probe launched by federal prosecutors in civilian courts.

Allegations by the soldiers that the SEALs tried to cover it all up reverberated across a Navy already reeling from multiple scandals, including the ongoing “Fat Leonard” Navy bribery case.

After the 2015 story in The New York Times, the Navy launched probes not only into what the SEALs allegedly did in Afghanistan but also the process Smith used to sidestep court-martial proceedings against them.

Smith’s name was scrubbed from a selection list for admiral, although prosecutors said Monday his delayed promotion now has been forwarded to the White House for approval.

In his Monday ruling, Cmdr. Gaston seized on actions taken against Smith, reasoning that they could have sent a “perceptible chill over the military criminal justice system” by warning future commanders that they also wouldn’t get promoted if they didn’t prosecute the SEALs.

“If it was known to (Rear Adm.) Losey it would be known to Szymanski when he took over,” Gaston said.

On Jan. 19, 2017, the three enlisted SEALs were charged with war crimes by Coronado-based Szymanski and nearly eight months later Navy Region Southwest commander Rear Adm. Yancy B. Lindsey forwarded their prosecutions to a general court-martial trial in San Diego.

The top military prosecutor in the war crimes case, Cmdr. Andrea Lockhart, vowed to press the Navy’s view that even if Crawford and others discussed the SEALs it doesn’t mean other commanders such as Szymanski and Lindsey failed to rely on evidence uncovered by news reporters and NCIS to make independent decisions to charge the commandos.The hearings resume on Tuesday morning.